Overview of clusters

The following table shows the numbers of prevalent vs. non-prevalent genes found in each cluster (first two columns), followed by the number of significantly enriched categories found in each cluster for each of the annotation sources found using the ORA method (remaining columns).

MF Over Representation Analysis

The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category. Pies proportion represent the proportion of genes belonging to each cluster.

This graph can not be plotted because fewer than two functional categories were enriched

BP Over Representation Analysis

The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category. Pies proportion represent the proportion of genes belonging to each cluster.

This graph can not be plotted because fewer than two functional categories were enriched

CC Over Representation Analysis

The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category. Pies proportion represent the proportion of genes belonging to each cluster.

This graph can not be plotted because fewer than two functional categories were enriched

KEGG Over Representation Analysis

The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

This graph can not be plotted because fewer than two functional categories were enriched

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category. Pies proportion represent the proportion of genes belonging to each cluster.

This graph can not be plotted because fewer than two functional categories were enriched

This graph can not be plotted because fewer than two functional categories were enriched

Reactome Over Representation Analysis

The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category. Pies proportion represent the proportion of genes belonging to each cluster.

This graph can not be plotted because fewer than two functional categories were enriched